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Targeted occupant surveys: A novel method to effectively relate occupant feedback with environmental conditions
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Data_Rcode for: American foulbrood in a honeybee colony: spore-symptom relationship and feedbacks between disease and colony development
<p>Original data and analysis (R code) for the publication</p> <p>Stephan JG, De Miranda JR, Forsgren E. (2020). American foulbrood in a honeybee colony: spore-symptom relationship and feedbacks between disease and colony development. BMC Ecology.</p>
Data from: Feedback cooling of a room temperature mechanical oscillator close to its motional groundstate
<p>Source data for figures.</p>
Effects of low-carbon energy adoption on airborne particulate matter concentrations with feedbacks to future climate over California
<p>California plans to reduce emissions of long-lived greenhouse gases (GHGs) through adoption of new energy systems that will also lower concentrations of short-lived absorbing soot contained in airborne particulate matter (PM). Here we examine the direct and indirect effects of reduced PM concentrations under a low-carbon energy (GHG-Step) scenario on radiative forcing in California. Simulations were carried out using the source-oriented WRF/Chem (SOWC) model over California with 12 km spatial resolution for the year 2054. The avoided aerosol emissions due to technology advances in the GHG-step scenario reduce ground level PM concentrations by ~8.85% over land compared to the Business as Usual (BAU) scenario, but changes to meteorological parameters are more modest. Top of atmospheric forcing predicted by the SOWC model increased by 0.15 W m<sup>-2</sup>, surface temperature warmed by 0.001 K, and planetary boundary layer height (PBLH) increased by 2.20 cm in the GHG-Step scenario compared to the BAU scenario. PM climate feedbacks are small because the significant changes in ground level PM concentrations associated with the GHG-Step scenario are limited to the first few hundred meters of the atmosphere, with little change for the majority of the vertical column above that level. As an order-of-magnitude comparison, the long-term effects of global reductions in GHG emissions (RCP8.5 – RCP4.5) lowered average surface temperature over the California study domain by approximately 0.76 K. The effects of long-lived climate pollutants such as CO<sub>2</sub> are much stronger than the effects of short-lived climate pollutants such as PM soot over California in the year 2054. </p>
Plant Biomass data from: Bottom-up Herbivore-Plant Feedbacks Trump Trophic Cascades in a Wolf-Elk-Grassland System
<p>Top-down predator-prey effects that alter the abundance, biomass, or productivity of a population community across more than one link in a food web are referred to as trophic cascades. While these effects have been extensively studied in aquatic environments, fewer studies have examined trophic cascades in terrestrial ecosystems. And fewer still terrestrial studies have tested for trophic cascades between vertebrates and grassland vegetation. Across the globe, grassland plant biomass is driven by both precipitation and non-linear positive feedbacks between grazing and plant productivity, as predicted by the Intermediate Grazing Hypothesis. Yet little is known about the role that apex carnivores play in regard to trophic impacts on grassland biomass. We utilized a long-term dataset collected over the last two decades on a montane rough-fescue grassland adjacent to Banff National Park, Alberta, to test whether top-down effects regulate grassland biomass in a wolf-elk system. First, we measured annual growing season plant biomass from 2006 – 2018 at 61 repeat sampled plots in the grassland. Next, we measured wolf predation risk using a previously developed wolf resource selection function created from GPS radiocollar data from 5 wolf packs. Finally, we measured grazing intensity using Brownian Bridge Movement Models derived from GPS radiocollar data from 131 unique elk. We then tested top-down, bottom-up and abiotic hypotheses for grassland biomass over time in program R. The top model incorporated precipitation and positive non-linear effects of elk use, excluding predator effects and thus failing to support the trophic cascade hypothesis. This may be due to the observational nature of this study, or predation effects in this system may be obscured by human use. Alternatively, our results also support the hypothesis that intermediate grazing may outweigh the benefits of predation in grassland systems. Our study serves to help fill a gap in trophic cascade literature, and emphasizes that positive feedback between grazers and grasslands may trump top-down effects. Understanding when trophic cascade theory is or is not applicable is vital for carnivore management, conservation, and reintroduction efforts across North America.</p>
Soil microbial legacy drives crop diversity advantage: linking ecological plant-soil feedback with agricultural intercropping
<ol> <li>Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant-soil feedback (PSF) theory and method, we quantified how much soil microbes contributed to intercropping overyielding and detected which microbial groups mediated this effect.</li> <li>Soils were collected as inocula and sequenced from a unique 10-year field experiment, consisting of monoculture, intercropping and rotation planted with wheat (<i>Triticum aestivum</i>), maize (<i>Zea mays</i>) or faba bean (<i>Vicia faba</i>). A PSF study was conducted to test microbial effects on three crops' growth in monoculture or intercropping.</li> <li>In wheat & faba bean (W&F) and maize & faba bean (M&F) systems, soil microbes drove intercropping overyielding compared to monoculture, with 28-51% of the overyielding contributed by microbial legacies. The overyielding effects resulted from negative PSFs in both systems, as crops, in particular faba bean grew better in soils conditioned by other crops than itself. Moreover, faba bean grew better in soils from intercropping or rotation than from the average of monocultures, indicating a strong positive legacy effect of multispecies cropping systems. However, with positive PSF and negative legacy benefit effect of intercropping/rotation, we did not observe significant overyielding in the W&M system.</li> <li>With more bacterial and fungal dissimilarities by metabarcoding in heterospecific than its own soil, the better it improved faba bean growth. More detailed analysis showed faba bean monoculture soil accumulated more putative pathogens with higher <i>Fusarium</i> relative abundance and more <i>Fusarium oxysporum</i> gene copies by qPCR, while in heterspecific soils, there was less pathogenetic effects when cereals were engaged. Further analysis in maize/faba bean intercropping also showed an increase of rhizobia relative abundance.</li> <li> <i>Synthesis and applications</i>. Our results demonstrate a soil microbiome-mediated advantage in intercropping through suppression of the negative PSF of pathogens and increasing beneficial microbes. As microbial mediation of overyielding is context-dependent, we conclude that the dynamics of both beneficial and pathogenic microbes should be considered in designing cropping systems for sustainable agriculture, particularly including combinations of legumes and cereals.</li> </ol>
Development of a Feedback Evaluation Tool for the Assessment of Telerehabilitation as a Teaching-Learning Tool for Medical Students Dataset
<p>Acknowledging that telemedicine is a growing medium of instruction, it is important for their be specific tools to measure student outcomes. This study aims to create a feedback evaluation tool to aid students express their concerns on telerehabilitation as a method of instruction, as well as aid the educators in receiving specific points to improve upon.</p> <p>The file attached is the collected data for the research on the Development of a Feedback Evaluation Tool for the Assessment of Telerehabilitation as a Teaching-Learning Tool for Medical Students. It contains the processed data from the Data Collection Forms as well as the results of the processed interview.</p>
Ag2S nanoheaters with multiparameter sensing for reliable thermal feedback during in vivo tumor therapy
<p>The emergence of luminescence nanothermometry in bio and nanomedicine has enabled achievements outside the reach of conventional techniques. For instance, it has provided real-time monitoring to in vivo thermal therapies of tumors, a mandatory requirement for these techniques to work safely and efficiently. However, the reliability of intratumoral thermal readings is currently in question due to the presence of artefacts caused by the inhomogeneous optical properties of biological tissues. This work demonstrates how it is possible to avoid, under specific conditions, these artefacts and reach precise and reliable in vivo intratumoral thermal feedback during in vivo photothermal treatments. The method proposed is based on the use of luminescent nanoparticles capable of multiparametric thermal sensing. The results demonstrate how the convergence of the different thermal readouts becomes a solid indicator of their reliability. It is shown how this new approach makes possible precise (thermal uncertainties below 1 °C) intratumoral thermal feed-back, while simple, efficient, and minimally invasive in vivo thermal treatments of surface tumors is carried out. Results included in this work provide an ingenious route toward the consolidation of luminescence nanothermometry as a convincing technique for high sensitivity preclinical thermal sensing, while also constituting a step toward improved photothermal therapies.</p>
Supplementary material 1 from: Häberlein L, Claas O (2020) Dataset: Feedback on the Path2Integrity learning cards for research integrity. Research Ideas and Outcomes 6: e58434. https://doi.org/10.3897/rio.6.e58434
Dataset: Feedback on the Path2Integrity learning cards for research integrity
Data from: Feeding evolution of a herbivore influences an arthropod community through plants: implications for plant-mediated eco-evolutionary feedback loop
1. Genetic variation in individual species can have important ecological consequences, and sometimes, these interactions are mediated through another species. For example, genetic variation in an herbivore could alter plant responses that then influence other plant-associated arthropods. However, few systems have experimentally tested the ecological consequences of genetic variation as mediated through other species, especially within the same trophic community context. 2. I studied how evolution of feeding preference in the willow leaf beetle (Plagiodera versicolora), which occurs under selection in a herbivore community context, feeds back to an arthropod community through plant-mediated indirect interactions. Previous studies show beetle populations locally adapt distinct preferences ranging from the gourmet-type, which feeds exclusively on new leaves of willows, to the no-preference (no-pref) type, which displays non-preferential feeding on leaves of different ages. 3. I conducted field experiments at two sites that mimicked evolutionary changes in the feeding preference of the leaf beetle. I manipulated the composition of leaf beetle feeding types for 6 days in spring and then investigated subsequent development of arthropod communities. I found that initial herbivory by a higher proportion of gourmet-type beetles led to lower subsequent abundance of conspecific beetle larvae. In contrast, a higher proportion of gourmet-type beetles resulted in higher abundance of aphids. Aphid-tending ants also increased with the increasing abundance of aphids. As a result, species diversity of arthropod communities decreased with the proportion of gourmet-type beetles in the initial beetle treatment. 4. Community assembly dynamics were significantly influenced by interactive effects between the initial beetle treatment and subsequent colonizer species identities. Thus, beetle genetic variation had long-lasting effects through a temporal chain of indirect interactions likely mediated through induced plant responses and the abundance of aphids. 5. Synthesis. Evolutionary changes in feeding traits within an herbivore species had profound but predictable impact on local arthropod communities. Because the feeding evolution of herbivores nearly always occurs in a community context, plant-mediated feedback loops between the evolution and ecological community of arthropods may be widespread in nature.
Data from: Complementarity and selection effects in early and mid-successional plant communities are differentially affected by plant-soil feedback
1. Many studies that provided evidence for a positive relationship between plant diversity and productivity have proposed that this effect may be explained by complementarity among species in resources utilization, or selection of particularly productive species in high-diversity plant communities. Recent studies have related the higher productivity in diverse plant communities to suppression of pathogenic soil biota. If soil biota plays a role in diversity–productivity relationships, the question remains about how they may influence complementarity and selection effects. 2. Here we examine how complementarity and selection effects may depend on soil biota using a plant–soil feedback approach. We used monocultures and mixtures of early successional plant species, which are known to have mostly negative plant–soil feedback effects, and mid-successional plant species, which generally have neutral plant–soil feedback. 3. We found that plant–soil feedback effects differed between monocultures and mixed plant communities, as well as between early and mid-successional plants. This resulted in a significant interaction effect between diversity and successional stage. In monocultures, plant–soil feedback tended to be negative for early and positive for mid-successional plant species. Interestingly, the community feedback responses of the mixed communities were opposite, being positive for early and negative for mid-successional community. 4. Plant–soil feedback differentially affected complementarity and selection effects of early and mid-successional plant communities: it enhanced complementarity effects of early and decreased selection effects of mid-successional species. 5. Synthesis. Soil biota that drive plant–soil feedback effects can influence the diversity–productivity relationship not only through decreased biomass production in monocultures compared to mixtures, but also through influencing complementarity and selection effects among species in mixed plant communities. Our results reveal that biodiversity–productivity relationships depend on plant–soil feedback interactions, which depend on the successional position of the plant. We propose that including successional position and trait-based analyses of plant–soil feedback in diversity-functioning studies will enhance understanding consequences of biodiversity loss for productivity and other ecosystem processes.
Data from: Coevolutionary feedbacks between family interactions and life history
Families with parental care show a parent–offspring conflict over the amount of parental investment. To date, the resolution of this conflict was modeled as being driven by either purely within-brood or between-brood competition. In reality the partitioning of parental resources within- versus between-broods is an evolving life history trait, which can be affected by parent–offspring interactions. This coevolutionary feedback between life history and family interactions may influence the evolutionary process and outcome of parent–offspring coadaptation. We used a genetic framework for a simulation model where we allowed parental parity to coevolve with traits that determine parental investment. The model included unlinked loci for clutch size, parental sensitivity, baseline provisioning, and offspring begging. The simulation showed that tight coadaptation of parent and offspring traits only occurred in iteroparous outcomes whereas semelparous outcomes were characterized by weak coadaptation. When genetic variation in clutch size was unrestricted in the ancestral population, semelparity and maximal begging with poor coadaptation evolved throughout. Conversely, when genetic variation was limited to iteroparous conditions, and/or when parental sensitivity was treated as an evolutionarily fixed sensory bias, coadapted outcomes were more likely. Our findings show the influence of a feedback between parity, coadaptation, and conflict on the evolution of parent–offspring interactions.
Data from: Emergence of weak‐intransitive competition through adaptive diversification and eco‐evolutionary feedbacks
Indirect biotic interactions—such as intransitive competition—are increasingly recognized as being important in shaping ecological patterns in natural systems. Over long time‐scales, such indirect interactions may affect the evolution of species phenotypes, which in turn can modify these interactions, thereby begetting eco‐evolutionary feedbacks. If indirect intransitive interactions can emerge in situ during lineage diversification, they could profoundly affect species' phenotypic diversity, temporal stability, and subsequent diversification rates. We address these questions by investigating the conditions under which indirect intransitive competition can emerge from a lineage diversifying in sympatry. We use an adaptive dynamics model to study the ecological and evolutionary properties of this lineage under different scenarios where competition for resources between phenotypes varies in strength and (a)symmetry. Results show that weak‐intransitive competition can emerge during the sympatric diversification of a single lineage. "Weak‐intransitivity" here refers to situations where species interactions are not perfectly transitive, that is, there is no strict hierarchy in species competitive abilities. The strength of such weak‐intransitivity increases when the competition between phenotypes increases in strength and asymmetry. The strength of intransitivity also correlates with other system properties. We notably found that the strength of intransitivity increases with the number of phenotypes, and that greater intransitivity correlates with the evolution of greater functional trait divergences between phenotypes, greater resistance to invasion by new phenotypes but lower resistance to disturbances as well as slower evolutionary rates. Synthesis. This theoretical exploration of the evolution of intransitive competition provides the first formal bridge between the ecological and evolutionary aspects of intransitive competition. We show that, when competitive interactions are strong enough, weak‐intransitive competition is more likely to emerge through adaptive diversification than from a random community assembly. Intransitive competition is, therefore, not only restricted to between‐species interactions but can also function as a regulator of diversification within species, thereby affecting lineage functional diversity, and ecological and evolutionary stability.
Data from: Epidemiological feedbacks affect evolutionary emergence of pathogens
The evolutionary emergence of new pathogens via mutation poses a considerable risk to human and animal populations. Most previous studies have investigated cases where a potentially pandemic strain emerges though mutation from an initial maladapted strain (i.e., its basic reproductive ratio R0 < 1). However, an alternative (and arguably more likely) cause of novel pathogen emergence is where a "weakly adapted" strain (with R0 ≈ 1) mutates into a strongly adapted strain (with R0 ≫ 1). In this case, a proportion of the host susceptible population is removed as the first strain spreads, but the impact this feedback has on emergence of mutated strains has yet to be quantified. We produce a model of pathogen emergence that takes into account changes in the susceptible population over time and find that the ongoing depletion of susceptible individuals by the first strain has a drastic effect on the emergence probability of the mutated strain, above that assumed by just scaling the reproductive ratio. Finally, we apply our model to the documented emergence of Chikungunya virus on La Réunion Island and demonstrate that the emergence probability of the mutated strain was reduced approximately 10-fold, compared to models assuming that susceptible depletion would not affect outbreak probability. These results highlight the importance of taking population feedbacks into account when predicting disease emergence.
Data from: Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations
Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated.
Data from: Reciprocal relationships between behaviour and parasites suggest that negative feedback may drive flexibility in male reproductive behaviour
Parasites are ubiquitous components of the environment that contribute to behavioral and life-history variation among hosts. Although it's well-known that host behavior can affect parasite infection risk and that parasites can alter host behavior, the potential for dynamic feedback between these processes is poorly characterized. Using Grant's gazelle (Nanger granti) as a model, we tested for reciprocal effects of behavior on parasites and parasites on behavior to understand whether behavior-parasite feedback could play a role in maintaining variation in male reproductive behavior. Adult male gazelles either defend territories to attract mates or reside in bachelor groups. Territoriality is highly variable both within- and between-individuals, suggesting that territory maintenance is costly. Using a combination of longitudinal and experimental studies, we found that individual males transition frequently between territorial and bachelor reproductive status, and that elevated parasite burdens are a cost of territoriality. Moreover, among territorial males, parasites suppress aspects of behavior related to territory maintenance and defense. These results suggest that territorial behavior promotes the accumulation of parasites in males, and these parasites dampen the very behaviors required for territory maintenance. Our findings suggest that reciprocal feedback between host behavior and parasitism could be a mechanism maintaining variation in male reproductive behavior in the system.
Data from: Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning
1.Plant-soil feedback (PSF) has been identified as a key driver of local plant diversity and evenness in competitive communities. However, while it has been shown that spatial PSF heterogeneity can alter plant performance and competitive interactions, there is no proof of principle that spatial PSF heterogeneity enhances community diversity. 2.Using a grassland model system we separated two aspects of spatial heterogeneity: the number of species conditioning the soil and spatial distribution of the PSFs. 3.Our data show that PSFs promoted a higher plant evenness when the soil was conditioned by multiple species (mixed-conditioned), then when the soil was conditioned by a single species (mono-conditioned). On mono-conditioned soils, heterospecifics typically outperformed the focal species. In addition, there was a trend for increasing community evenness from uniform, via fine-grained to coarse-grained mixed-conditioned soils, but this was not significant. 4.On mixed-conditioned soils, performance of all competing species was intermediate to the best and the worst mono-conditioned soils, leading to higher community evenness. 5.Our data demonstrate that PSFs play a role in promoting plant evenness. Across mono-conditioned soils, PSF led to altered competitive hierarchies. However, on soils conditioned by multiple species, competitive ability among species was more similar and this led to higher plant evenness. The spatial distribution of the heterogeneity, on the other hand, did not significantly affect plant evenness. Our data therefore show that community evenness was more strongly related to the number of plant species that conditioned the soil than the spatial distribution of the PSF heterogeneity. Future studies need to investigate the importance of PSFs in the field across plant life-stages and multiple generations.
Data from: Plant competition alters the temporal dynamics of plant-soil feedbacks
1. Most studies on plant-soil feedback (PSF) and plant competition measure the feedback response at one moment only. However, PSFs and competition may both change over time, and how PSF and competition interact over time is unclear. 2. We tested the temporal dynamics of PSF and interspecific competition for the forb Jacobaea vulgaris and the grass Holcus lanatus. We grew both species individually and in interspecific competition in soil that was first conditioned in the greenhouse by J. vulgaris, by H. lanatus or without plant growth. For a period of 11 weeks, we harvested plants twice a week and analyzed the fungal and chemical composition of the different soils at the end of the first and second growth phase. 3. During the second growth phase, when grown in isolation, both species produced more biomass in heterospecific conditioned soil than in conspecific conditioned soil. Young J. vulgaris exhibited a strong negative conspecific feedback, but this effect diminished over time and became neutral in older plants. In contrast, when grown in competition, the negative conspecific feedback of J. vulgaris exacerbated over time. Older H. lanatus plants benefited more from heterospecific conditioning when competing with J. vulgaris, then when grown isolated. 4. Fungal community composition and soil chemistry differed significantly between soils but this was mainly driven by differences between plant-conditioned and unconditioned soils. Remarkably, at the end of the second growth phase, fungal community composition was not explained by the legacy of the species that had been grown in the soil most recently, but still reflected the legacy of the first growth phase. We reexamined plant growth during a third growth phase. Biomass of J. vulgaris was still influenced by the treatments imposed during the first phase, while H. lanatus responded only to the plant growth treatments imposed during the second phase. 5. Synthesis: Our study shows that the direction and magnitude of PSF depends on plant age and competition but also on soil legacy effects of earlier plant growth. These results highlight the need to incorporate dynamic PSFs in research on plant populations and communities.
Data from: Eco-evolutionary feedbacks during experimental range expansions
Understanding biological range expansions and invasions is of great ecological and economical interest. Importantly, spatial dynamics can be deeply affected by rapid evolution depending on the ecological context. Using experimental evolution in replicated microcosm landscapes and numerical analyses we show experimentally that the ecological process of range expansions leads to the evolution of increased dispersal. This evolutionary change counter-intuitively feeds back on (macro-)ecological patterns affecting the spatial distribution of population densities. While existing theory suggests that densities decrease from range cores to range margins due to K-selection, we show the reverse to be true when competition is considered explicitly including resource dynamics. We suggest that a dispersal-foraging trade-off, leading to more 'prudent' foraging at range margins, is the driving mechanism behind the macroecological pattern reported. In conclusion, rapid multi-trait evolution and eco-evolutionary feedbacks are highly relevant for understanding macroecological patterns and designing appropriate conservation strategies.
Data from: Invasion-mediated effects on marine trophic interactions in a changing climate: positive feedbacks favour kelp persistence
The interactive effects of ocean warming and invasive species are complex and remain a source of uncertainty for projecting future ecological change. Climate-mediated change to trophic interactions can have pervasive ecological consequences, but the role of invasion in mediating trophic effects is largely unstudied. Using manipulative experiments in replicated outdoor mesocosms, we reveal how near-future ocean warming and macrophyte invasion scenarios interactively impact gastropod grazing intensity and preference for consumption of foundation macroalgae (Ecklonia radiata and Sargassum vestitum). Elevated water temperature increased consumption of both macroalgae through greater grazing intensity. Given the documented decline of kelp (E. radiata) growth at higher water temperatures, enhanced grazing could contribute to the shift from kelp-dominated to Sargasssum-dominated reefs that is occurring at the low-latitude margins of kelp distribution. However, presence of a native invader (Caulerpa filiformis) was related to low consumption by the herbivores on dominant kelp at warmer temperatures. Thus, antagonistic effects between climate change and a range expanding species can favour kelp persistence in a warmer future. Introduction of species should, therefore, not automatically be considered unfavourable under climate change scenarios. Climatic changes are increasing the need for effective management actions to address the interactive effects of multiple stressors and their ecological consequences, rather than single threats in isolation.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.